Sodium in PDB 1mvo: Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis

The structure of Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis, PDB code: 1mvo was solved by C.Birck, Y.Chen, F.M.Hulett, J.P.Samama, Structural Proteomicsin Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.00 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.704, 45.704, 134.811, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.2

The structure of Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis (pdb code 1mvo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis, PDB code: 1mvo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:16.3 occ:1.00 O A:HOH372 2.0 34.0 1.0 O A:HOH375 2.0 40.6 1.0 O A:HOH364 2.1 37.6 1.0 OE2 A:GLU37 2.2 24.7 1.0 O A:HOH356 2.2 25.4 1.0 O A:HOH355 2.2 24.1 1.0 CD A:GLU37 3.1 21.2 1.0 OE1 A:GLU37 3.4 19.4 1.0 O A:HOH215 4.0 30.3 1.0 NZ A:LYS41 4.2 25.6 1.0 O A:THR31 4.4 16.6 1.0 CG A:GLU37 4.5 17.6 1.0 O A:HOH334 4.5 35.8 1.0 O A:HOH234 4.8 28.7 1.0 OG1 A:THR31 5.0 20.2 1.0 OG A:SER33 5.0 20.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Phop Receiver Domain From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:17.7 occ:1.00 O A:PHE75 2.2 14.5 1.0 O A:GLY96 2.3 17.0 1.0 O A:HOH246 2.3 29.1 1.0 OD2 A:ASP98 2.4 18.0 1.0 O A:HOH253 2.4 21.4 1.0 C A:PHE75 3.3 13.5 1.0 CG A:ASP98 3.4 20.1 1.0 C A:GLY96 3.4 16.2 1.0 OD1 A:ASP98 3.6 25.6 1.0 O A:HOH298 3.7 42.3 1.0 CA A:GLY96 3.9 15.9 1.0 CA A:PRO76 4.0 13.3 1.0 N A:PRO76 4.0 13.7 1.0 N A:ILE77 4.0 11.9 1.0 N A:PHE75 4.2 13.5 1.0 CD1 A:ILE77 4.2 15.5 1.0 CG1 A:ILE77 4.3 14.1 1.0 O A:HOH239 4.3 26.7 1.0 O A:HOH281 4.4 36.1 1.0 C A:PRO76 4.4 12.8 1.0 CA A:PHE75 4.4 13.8 1.0 CB A:ILE77 4.5 12.9 1.0 N A:ALA97 4.5 16.3 1.0 CG A:MET74 4.6 21.4 1.0 O A:HOH205 4.6 17.5 1.0 C A:ALA97 4.7 17.3 1.0 N A:ASP98 4.7 16.0 1.0 CB A:ASP98 4.7 17.2 1.0 CA A:ALA97 4.7 16.7 1.0 CA A:ILE77 4.9 12.0 1.0

C.Birck, Y.Chen, F.M.Hulett, J.P.Samama. The Crystal Structure of the Phosphorylation Domain in Phop Reveals A Functional Tandem Association Mediated By An Asymmetric Interface J.Bacteriol. V. 185 254 2003.
ISSN: ISSN 0021-9193
PubMed: 12486062
DOI: 10.1128/JB.185.1.254-261.2003